User: vchris_ngs

I did my PhD in the field of Cancer Biology employing NGS tools(publicly available) or ad-hoc development and analysing them. Mostly I do benchmarking of tools till I find the best fit for the heterogeneous cancer data. I work on integrating multi omics data and slowly now am venturing in field of single cell which is pretty interesting to me as of now. Battling with two of my worst fears Biology and computer science to give life a better meaning. My first fear made me push to get the PhD and now I want to drive the improvements in the field. The challenge in life science and technology drives me and so I am pursuing the research field. Everyday is a new learning and knowledge is never ending. Biostars helped me learn all along and now with my experience and learning am happy to help others.

Posts by vchris_ngs

... So these are Refseq ID. What do you want to do with the annotation and which species they belong to? geneSCG is clustering them based on functional relevance but these are too many ids, probably the entire transcriptome. Tell specifically the aim of the design and what you want to perform. ...

... It is used for dimensionality reduction and now depending upon variables and your interest of inferencing the applications will be considered. PCA has been a pretty favorite tool till date for RNA-Seq , ChIP-Seq and also WES data, but with incoming scRNASeq and also large scale SNPs data scoring pop ...

... I can suggest some links that will give you the flavor of both the methods that are used in dimensionality reduction.
1. [Link1][1]
2. [Link2][2]
3. If w.r.t scRNA-Seq check [here][3]
4. For bulk RNASeq check [here][4]
5. If you are a fan of kaggle this [link][5] is pretty fun as well for usag ...

... I totally agree how the hoopla over "Google AI solved genomics!" is on. At the end of the day it is a product they are bringing and pretty sure the buzz will be more than what it actually preaches. Having said that, I will feel it is worth taking a look at it as to how germline calls are made and im ...

... I agree to that but OP need to clarify if the QC reports of fastq was problematic or not or let's say the alignment. Problems can be a lot but if the OP is starting with exploratory analysis on counts then filtering is not to be ruled out. Only if it reduces the expression to a lot then it is big re ...

... It is a scenario which happens for non-coding RNAs but also true for protein-coding mRNA transcripts as well if the library is not done well or library enrichment is not in accordance with the kind of regions one is looking for. Another problem is are you quantifying across whole genome or only tran ...